update readme

README.md

@@ -54,6 +54,8 @@ Clair3 is the 3<sup>rd</sup> generation of [Clair](https://github.com/HKU-BAL/Cl
 
 ## Latest Updates
 
+*v0.1-r8 (Nov 11)* : 1. Added the `--enable_phasing` option that adds a step after Clair3 calling to output variants phased by WhatsHap ([#63](https://github.com/HKU-BAL/Clair3/issues/63)). 2. Fixed unexpected program termination on successful runs.
+
 *v0.1-r7 (Oct 18)* : 1. Increased `var_pct_full` in ONT mode from 0.3 to 0.7. Indel F1-score increased ~0.2%, but took ~30 minutes longer to finish calling a ~50x ONT dataset. 2. Expand fall through to next most likely variant if network prediction has insufficient read coverage ([#53](https://github.com/HKU-BAL/Clair3/pull/53) commit 09a7d185, contributor @[ftostevin-ont](https://github.com/ftostevin-ont)), accuracy improved on complex Indels. 3. Streamized pileup and full-alignment training workflows. Reduce diskspace demand in model training ([#55](https://github.com/HKU-BAL/Clair3/pull/55) commit 09a7d185, contributor @[ftostevin-ont](https://github.com/ftostevin-ont)). 4.  Added `mini_epochs` option in Train.py, performance  slightly improved in training a model for ONT Q20 data using mini-epochs([#60](https://github.com/HKU-BAL/Clair3/pull/60), contributor @[ftostevin-ont](https://github.com/ftostevin-ont)). 5. Massively reduced disk space demand when outputting GVCF. Now compressing GVCF intermediate files with lz4, five times smaller with little speed penalty. 6. Added `--remove_intermediate_dir`to remove intermediate files as soon as no longer needed ([#48](https://github.com/HKU-BAL/Clair3/issues/48)). 7. Renamed ONT pre-trained models with [Medaka](https://github.com/nanoporetech/medaka/blob/master/medaka/options.py#L22)'s naming convention. 8. Fixed training data spilling over to validation data ([#57](https://github.com/HKU-BAL/Clair3/issues/57)).
 
 *ONT-provided Models (Sep 23)*: ONT also provides Clair3 models for specific chemistries and basecallers through [Rerio](https://github.com/nanoporetech/rerio).
@@ -353,6 +355,7 @@ docker run -it hkubal/clair3:latest /opt/bin/run_clair3.sh --help
       --print_ref_calls         Show reference calls (0/0) in vcf file, default: disable.
       --include_all_ctgs        Call variants on all contigs, otherwise call in chr{1..22,X,Y} and {1..22,X,Y}, default: disable.
       --gvcf                    Enable GVCF output, default: disable.
+      --enable_phasing          Output phased variants using whatshap, default: disable.
       --remove_intermediate_dir Remove intermediate directory, including intermediate phased BAM, pileup and full-alignment results. default: disable.
       --snp_min_af=FLOAT        Minimum SNP AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.08,hifi:0.08,ilmn:0.08.
       --indel_min_af=FLOAT      Minimum INDEL AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.15,hifi:0.08,ilmn:0.08.